In this paper, a machine learning algorithm is applied to find a ferrite core structure with high magnetic coupling between transmitting (Tx) and receiving (Rx) coils for an electric vehicle (EV) wireless charging system. Since formula-based theoretical design is not available due to the non-linear magnetic field distortion stems from the presence of the ferrite core in an inductive power transfer (IPT) system, the proposed core structure design has been achieved through finite element analysis (FEA) simulation-based data learning. The proposed design methods are so general that they can be applied to any conventional IPT coil design. By training only 0.011 % data out of the total possible cases, it is verified by simulation and experiment that the ferrite core structure obtained by the proposed method has a mutual inductance that is 0.6 % higher than that of the conventional design level in the case of 15 cm distance between the Tx and Rx coils, even though the volume of the ferrite cores are reduced to 90 %. Also, a prototype 3.0 kW stationary EV wireless charging system was implemented and showed fairly better performance than a conventional case.